NAME
samtools-dict - create a sequence dictionary file from a fasta file
SYNOPSIS
samtools dict ref.fasta|ref.fasta.gz
DESCRIPTION
Create a sequence dictionary file from a fasta file.
OPTIONS
-a, --assembly STR
Specify the assembly for the AS tag.
-A, --alias, --alternative-name
Add an AN tag with the same value as the SN tag, except that a “chr” prefix is removed if SN has one or added if it does not. For mitochondria (i.e., when SN is “M” or “MT”, with or without a “chr” prefix), also adds the remaining combinations of “chr/M/MT” to the AN tag.
-H, --no-header
Do not print the @HD header line.
-l, --alt FILE
Add an AH tag to each sequence listed in the specified bwa(1)-style .alt file. These files use SAM records to represent alternate locus sequences (as named in the QNAME field) and their mappings to the primary assembly.
-o, --output FILE
Output to FILE [stdout].
-s, --species STR
Specify the species for the SP tag.
-u, --uri STR
Specify the URI for the UR tag. Defaults to the absolute path of ref.fasta unless reading from stdin.
AUTHOR
Written by Shane McCarthy from the Sanger Institute.
SEE ALSO
samtools(1), bcftools(1), bwa(1), sam(5), tabix(1)
Samtools
website: <http://www.htslib.org/>;
File format specification of SAM/BAM,CRAM,VCF/BCF:
<http://samtools.github.io/hts-specs>;
Samtools latest source:
<https://github.com/samtools/samtools>;
HTSlib latest source:
<https://github.com/samtools/htslib>;
Bcftools website:
<http://samtools.github.io/bcftools>;